From 236e5c6d215661e94bdc12b9d4eda5f585fa66b3 Mon Sep 17 00:00:00 2001 From: Toni G <toni.giorgino@gmail.com> Date: Thu, 22 May 2014 14:52:13 +0200 Subject: [PATCH] Added shameless plug about generating PATH reference files with Plumed-GUI --- user-doc/tutorials/belfast-2.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/user-doc/tutorials/belfast-2.txt b/user-doc/tutorials/belfast-2.txt index 8b06b3985..f99bed68c 100644 --- a/user-doc/tutorials/belfast-2.txt +++ b/user-doc/tutorials/belfast-2.txt @@ -340,6 +340,7 @@ fix is someway. My preference is to dump the whole pdb but water (when I do not which have zero occupancy will not be used in the alignment. The second column is beta and controls which atoms are used for the calculation of the distance after having performed the alignment on the set of atoms which have nonzero occupancy column. In this way you can align all your system by using a part of the system and calculate the distance respect to another set. This is handy in case of protein-ligand. You set the alignment of the protein and you calculate the distance based on the ligand and the part of the protein which is in contact with the protein. This is done for example in <a href="http://pubs.acs.org/doi/abs/10.1021/jp911689r">this article</a>. +- <a href="http://www.multiscalelab.org/utilities/PlumedGUI">Plumed-GUI</a> (version \> 2.0) provides the <em>Structure->Build reference structure...</em> function to generate inputs that conform to the above rules from within VMD. - Note that all the atoms contained in the REFERENCE must be the same. You cannot have a variable number of atoms in each pdb contained in the reference. - The reference is composed as a set of concatenated PDBs that are interrupted by a TER/END/ENDMDL card. Both HETATM and ATOM cards denote the atoms of the set. - Include in the reference frames only the needed atoms. For example, if you have a methyl group involved in a conformational transition, it might be that you do not want to include the hydrogen atoms of the methyl since these rotate fast and probably they do not play ant relevant role. -- GitLab